Change search
Refine search result
12345 101 - 150 of 210
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 101. Klepsatel, Peter
    et al.
    Wildridge, David
    Gáliková, Martina
    Stockholm University, Faculty of Science, Department of Zoology.
    Temperature induces changes in Drosophila energy stores2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 5239Article in journal (Refereed)
    Abstract [en]

    Temperature has a profound impact on animal physiology. In this study, we examined the effect of ambient temperature on the energy stores of the model organism Drosophila melanogaster. By exposing adult males to 11 temperatures between 13 degrees C and 33 degrees C, we found that temperature significantly affects the amount of energy reserves. Whereas flies increase their fat stores at intermediate temperatures, exposure to temperatures below 15 degrees C or above 27 degrees C causes a reduction of fat reserves. Moreover, we found that glycogen stores followed a similar trend, although not so pronounced. To elucidate the underlying mechanism of these changes, we compared the temperature dependence of food consumption and metabolic rate. This analysis revealed that food intake and metabolic rate scale with temperature equally, suggesting that the temperature-induced changes in energy reserves are probably not caused by a mismatch between these two traits. Finally, we assessed the effect of temperature on starvation resistance. We found that starvation survival is a negative exponential function of temperature; however we did not find any clear evidence that implies the relative starvation resistance is compromised at non-optimal temperatures. Our results indicate that whilst optimal temperatures can promote accumulation of energy reserves, exposure to non-optimal temperatures reduces Drosophila energy stores.

  • 102. Kocjan, Andraž
    et al.
    Logar, Manca
    Shen, Zhijian
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    The agglomeration, coalescence and sliding of nanoparticles, leading to the rapid sintering of zirconia nanoceramics2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 2541Article in journal (Refereed)
    Abstract [en]

    Conventional sintering is a time- and energy-consuming process used for the densification of consolidated particles facilitated by atomic diffusion at high temperatures. Nanoparticles, with their increased surface free energy, can promote sintering; however, size reduction also promotes agglomeration, so hampering particle packing and complete densification. Here we show how the ordered agglomeration of zirconia primary crystallites into secondary particle assemblies ensures their homogeneous packing, while also preserving the high surface energy to higher temperatures, increasing the sintering activity. When exposed to intense electromagnetic radiation, providing rapid heating, the assembled crystallites are subjected to further agglomeration, coalescence and sliding, leading to rapid densification in the absence of extensive diffusional processes, cancelling out the grain growth during the initial sintering stages and providing a zirconia nanoceramic in only 2 minutes at 1300 degrees C.

  • 103. Korolev, Nikolay
    et al.
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Nordenskiöld, Lars
    A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 1543Article in journal (Refereed)
    Abstract [en]

    Chromatin condensation is driven by the energetically favourable interaction between nucleosome core particles (NCPs). The close NCP-NCP contact, stacking, is a primary structural element of all condensed states of chromatin in vitro and in vivo. However, the molecular structure of stacked nucleosomes as well as the nature of the interactions involved in its formation have not yet been systematically studied. Here we undertake an investigation of both the structural and physico-chemical features of NCP structure and the NCP-NCP stacking. We introduce an NCP-centred set of parameters (NCP-NCP distance, shift, rise, tilt, and others) that allows numerical characterisation of the mutual positions of the NCPs in the stacking and in any other structures formed by the NCP. NCP stacking in more than 140 published NCP crystal structures were analysed. In addition, coarse grained (CG) MD simulations modelling NCP condensation was carried out. The CG model takes into account details of the nucleosome structure and adequately describes the long range electrostatic forces as well as excluded volume effects acting in chromatin. The CG simulations showed good agreement with experimental data and revealed the importance of the H2A and H4 N-terminal tail bridging and screening as well as tail-tail correlations in the stacked nucleosomes.

  • 104. Krama, Tatjana
    et al.
    Vrublevska, Jolanta
    Freeberg, Todd M.
    Kullberg, Cecilia
    Stockholm University, Faculty of Science, Department of Zoology.
    Rantala, Markus J.
    Krams, Indrikis
    You mob my owl, I'll mob yours: birds play tit-for-tat game2012In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 2, article id 800Article in journal (Refereed)
    Abstract [en]

    Reciprocity is fundamental to cooperative behaviour and has been verified in theoretical models. However, there is still limited experimental evidence for reciprocity in non-primate species. Our results more decisively clarify that reciprocity with a tit-for-tat enforcement strategy can occur among breeding pied flycatchers Ficedula hypoleuca separate from considerations of byproduct mutualism. Breeding pairs living in close proximity (20-24 m) did exhibit byproduct mutualism and always assisted in mobbing regardless of their neighbours' prior actions. However, breeding pairs with distant neighbours (69-84 m) either assisted or refused to assist in mobbing a predatory owl based on whether or not the distant pair had previously helped them in their own nest defense against the predator. Clearly, these birds are aware of their specific spatial security context, remember their neighbours' prior behaviour, and choose a situation-specific strategic course of action, which could promote their longer-term security, a capacity previously thought unique to primates.

  • 105. Kumar, Pradeep
    et al.
    Wikfeldt, Thor Kjartan
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). University of Iceland, Iceland.
    Schlesinger, Daniel
    Stockholm University, Faculty of Science, Department of Physics.
    Pettersson, Lars G. M.
    Stockholm University, Faculty of Science, Department of Physics.
    Stanley, H. Eugene
    The Boson peak in supercooled water2013In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 3, article id 1980Article in journal (Refereed)
    Abstract [en]

    We perform extensive molecular dynamics simulations of the TIP4P/2005 model of water to investigate the origin of the Boson peak reported in experiments on supercooled water in nanoconfined pores, and in hydration water around proteins. We find that the onset of the Boson peak in supercooled bulk water coincides with the crossover to a predominantly low-density-like liquid below the Widom line T-W. The frequency and onset temperature of the Boson peak in our simulations of bulk water agree well with the results from experiments on nanoconfined water. Our results suggest that the Boson peak in water is not an exclusive effect of confinement. We further find that, similar to other glass-forming liquids, the vibrational modes corresponding to the Boson peak are spatially extended and are related to transverse phonons found in the parent crystal, here ice Ih.

  • 106. Kurrikoff, Kaido
    et al.
    Veiman, Kadi-Liis
    Künnapuu, Kadri
    Peets, Elin Madli
    Lehto, Tõnis
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Pärnaste, Ly
    Arukuusk, Piret
    Langel, Ülo
    Stockholm University, Faculty of Science, Department of Neurochemistry. University of Tartu, Estonia.
    Effective in vivo gene delivery with reduced toxicity, achieved by charge and fatty acid -modified cell penetrating peptide2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 17056Article in journal (Refereed)
    Abstract [en]

    Non-viral gene delivery systems have gained considerable attention as a promising alternative to viral delivery to treat diseases associated with aberrant gene expression. However, regardless of extensive research, only a little is known about the parameters that underline in vivo use of the nanoparticle-based delivery vectors. The modest efficacy and low safety of non-viral delivery are the two central issues that need to be addressed. We have previously characterized an efficient cell penetrating peptide, PF14, for in vivo applications. In the current work, we first develop an optimized formulation of PF14/pDNA nanocomplexes, which allows removal of the side-effects without compromising the bioefficacy in vivo. Secondly, based on the physicochemical complex formation studies and biological efficacy assessments, we develop a series of PF14 modifications with altered charge and fatty acid content. We show that with an optimal combination of overall charge and hydrophobicity in the peptide backbone, in vivo gene delivery can be augmented. Further combined with the safe formulation, systemic gene delivery lacking any side effects can be achieved.

  • 107. Kuzmenko, Anton
    et al.
    Derbikova, Ksenia
    Salvatori, Roger
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Tankov, Stoyan
    Atkinson, Gemma C.
    Tenson, Tanel
    Ott, Martin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Kamenski, Piotr
    Hauryliuk, Vasili
    Aim-less translation: loss of Saccharomyces cerevisiae mitochondrial translation initiation factor mIF3/Aim23 leads to unbalanced protein synthesis2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 18749Article in journal (Refereed)
    Abstract [en]

    The mitochondrial genome almost exclusively encodes a handful of transmembrane constituents of the oxidative phosphorylation (OXPHOS) system. Coordinated expression of these genes ensures the correct stoichiometry of the system's components. Translation initiation in mitochondria is assisted by two general initiation factors mIF2 and mIF3, orthologues of which in bacteria are indispensible for protein synthesis and viability. mIF3 was thought to be absent in Saccharomyces cerevisiae until we recently identified mitochondrial protein Aim23 as the missing orthologue. Here we show that, surprisingly, loss of mIF3/Aim23 in S. cerevisiae does not indiscriminately abrogate mitochondrial translation but rather causes an imbalance in protein production: the rate of synthesis of the Atp9 subunit of F1F0 ATP synthase (complex V) is increased, while expression of Cox1, Cox2 and Cox3 subunits of cytochrome c oxidase (complex IV) is repressed. Our results provide one more example of deviation of mitochondrial translation from its bacterial origins.

  • 108.
    Kylander, Malin E.
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Martinez-Cortizas, A.
    Bindler, Richard
    Kaal, Joeri
    Sjöström, Jenny K.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Hansson, Sophia V.
    Silva-Sanchez, Noemi
    Greenwood, Sarah L.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Gallagher, Kerry
    Rydberg, Johan
    Mörth, Carl-Magnus
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Rauch, Sebastien
    Mineral dust as a driver of carbon accumulation in northern latitudes2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 6876Article in journal (Refereed)
    Abstract [en]

    Peatlands in northern latitudes sequester one third of the world's soil organic carbon. Mineral dusts can affect the primary productivity of terrestrial systems through nutrient transport but this process has not yet been documented in these peat-rich regions. Here we analysed organic and inorganic fractions of an 8900-year-old sequence from Store Mosse (the Great Bog) in southern Sweden. Between 5420 and 4550 cal yr BP, we observe a seven-fold increase in net peat-accumulation rates corresponding to a maximum carbon-burial rate of 150 g C m(-2) yr(-1) -more than six times the global average. This high peat accumulation event occurs in parallel with a distinct change in the character of the dust deposited on the bog, which moves from being dominated by clay minerals to less weathered, phosphate and feldspar minerals. We hypothesize that this shift boosted nutrient input to the bog and stimulated ecosystem productivity. This study shows that diffuse sources and dust dynamics in northern temperate latitudes, often overlooked by the dust community in favour of arid and semi-arid regions, can be important drivers of peatland carbon accumulation and by extension, global climate, warranting further consideration in predictions of future climate variability.

  • 109.
    Kılınç, Gülşah Merve
    et al.
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Kashuba, Natalija
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies. University of Oslo, Museum of Cultural History, Norway.
    Yaka, Reyhan
    Sümer, Arev Pelin
    Yüncü, Eren
    Shergin, Dmitrij
    Ivanov, Grigorij Leonidovich
    Kichigin, Dmitrii
    Pestereva, Kjunnej
    Volkov, Denis
    Mandryka, Pavel
    Kharinskii, Artur
    Tishkin, Alexey
    Ineshin, Evgenij
    Kovychev, Evgeniy
    Stepanov, Aleksandr
    Alekseev, Aanatolij
    Fedoseeva, Svetlana Aleksandrovna
    Somel, Mehmet
    Jakobsson, Mattias
    Krzewińska, Maja
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Storå, Jan
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Götherström, Anders
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Investigating Holocene human population history in North Asia using ancient mitogenomes2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 8969Article in journal (Refereed)
    Abstract [en]

    Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c. 13,790 BP and c. 1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.

  • 110. Lebreton, Sébastien
    et al.
    Trona, Federica
    Borrero-Echeverry, Felipe
    Bilz, Florian
    Grabe, Veit
    Becher, Paul G.
    Carlsson, Mikael A.
    Stockholm University, Faculty of Science, Department of Zoology.
    Nässel, Dick R.
    Stockholm University, Faculty of Science, Department of Zoology.
    Hansson, Bill S.
    Sachse, Silke
    Witzgall, Peter
    Feeding regulates sex pheromone attraction and courtship in Drosophila females2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 13132Article in journal (Refereed)
    Abstract [en]

    In Drosophila melanogaster, gender-specific behavioural responses to the male-produced sex pheromone cis-vaccenyl acetate (cVA) rely on sexually dimorphic, third-order neural circuits. We show that nutritional state in female flies modulates cVA perception in first-order olfactory neurons. Starvation increases, and feeding reduces attraction to food odour, in both sexes. Adding cVA to food odour, however, maintains attraction in fed females, while it has no effect in males. Upregulation of sensitivity and behavioural responsiveness to cVA in fed females is paralleled by a strong increase in receptivity to male courtship. Functional imaging of the antennal lobe (AL), the olfactory centre in the insect brain, shows that olfactory input to DA1 and VM2 glomeruli is also modulated by starvation. Knocking down insulin receptors in neurons converging onto the DA1 glomerulus suggests that insulin-signalling partly controls pheromone perception in the AL, and adjusts cVA attraction according to nutritional state and sexual receptivity in Drosophila females.

  • 111. Lecoeur, Julien
    et al.
    Dacke, Marie
    Floreano, Dario
    Baird, Emily
    Stockholm University, Faculty of Science, Department of Zoology. Lund University, Sweden.
    The role of optic flow pooling in insect flight control in cluttered environments2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 7707Article in journal (Refereed)
    Abstract [en]

    Flight through cluttered environments, such as forests, poses great challenges for animals and machines alike because even small changes in flight path may lead to collisions with nearby obstacles. When flying along narrow corridors, insects use the magnitude of visual motion experienced in each eye to control their position, height, and speed but it is unclear how this strategy would work when the environment contains nearby obstacles against a distant background. To minimise the risk of collisions, we would expect animals to rely on the visual motion generated by only the nearby obstacles but is this the case? To answer this, we combine behavioural experiments with numerical simulations and provide the first evidence that bumblebees extract the maximum rate of image motion in the frontal visual field to steer away from obstacles. Our findings also suggest that bumblebees use different optic flow calculations to control lateral position, speed, and height.

  • 112.
    Lehmann, Philipp
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. University of Jyväskylä, Finland.
    Boratynski, Zbyszek
    Mappes, Tapio
    Mousseau, Timothy A.
    Møller, Anders P.
    Fitness costs of increased cataract frequency and cumulative radiation dose in natural mammalian populations from Chernobyl2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 19974Article in journal (Refereed)
    Abstract [en]

    A cataract is a clouding of the lens that reduces light transmission to the retina, and it decreases the visual acuity of the bearer. The prevalence of cataracts in natural populations of mammals, and their potential ecological significance, is poorly known. Cataracts have been reported to arise from high levels of oxidative stress and a major cause of oxidative stress is ionizing radiation. We investigated whether elevated frequencies of cataracts are found in eyes of bank voles Myodes glareolus collected from natural populations in areas with varying levels of background radiation in Chernobyl. We found high frequencies of cataracts in voles collected from different areas in Chernobyl. The frequency of cataracts was positively correlated with age, and in females also with the accumulated radiation dose. Furthermore, the number of offspring in female voles was negatively correlated with cataract severity. The results suggest that cataracts primarily develop as a function of ionizing background radiation, most likely as a plastic response to high levels of oxidative stress. It is therefore possible that the elevated levels of background radiation in Chernobyl affect the ecology and fitness of local mammals both directly through, for instance, reduced fertility and indirectly, through increased cataractogenesis.

  • 113. Lerche, Michael
    et al.
    Dian, Cyril
    Round, Adam
    Lönneborg, Rosa
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Brzezinski, Peter
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Leonard, Gordon A.
    The solution configurations of inactive and activated DntR have implications for the sliding dimer mechanism of LysR transcription factors2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 19988Article in journal (Refereed)
    Abstract [en]

    LysR Type Transcriptional Regulators (LTTRs) regulate basic metabolic pathways or virulence gene expression in prokaryotes. Evidence suggests that the activation of LTTRs involves a conformational change from an inactive compact apo-configuration that represses transcription to an active, expanded holo-form that promotes it. However, no LTTR has yet been observed to adopt both configurations. Here, we report the results of structural studies of various forms of the LTTR DntR. Crystal structures of apo-DntR and of a partially autoinducing mutant H169T-DntR suggest that active and inactive DntR maintain a compact homotetrameric configuration. However, Small Angle X-ray Scattering (SAXS) studies on solutions of apo-, H169T- and inducer-bound holo-DntR indicate a different behaviour, suggesting that while apo- DntR maintains a compact configuration in solution both H169T- and holo-DntR adopt an expanded conformation. Models of the SAXS-obtained solution conformations of apo- and holo-DntR homotetramers in complex with promoter-operator region DNA are consistent with previous observations of a shifting of LTTR DNA binding sites upon activation and a consequent relaxation in the bend of the promoter-operator region DNA. Our results thus provide clear evidence at the molecular level which strongly supports the 'sliding dimer' hypothesis concerning LTTR activation mechanisms.

  • 114. Li, Dianxiang
    et al.
    Luan, Yuanyuan
    Wang, Lei
    Qi, Mei
    Wang, Jinxing
    Xu, Jidong
    Arefin, Badrul
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Li, Meixia
    Expression of the Shrimp wap gene in Drosophila elicits defense responses and protease inhibitory activity2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 8779Article in journal (Refereed)
    Abstract [en]

    The wap gene encodes a single whey acidic protein (WAP) domain-containing peptide from Chinese white shrimp (Fenneropenaeus chinensis), which shows broad-spectrum antimicrobial activities and proteinase inhibitory activities in vitro. To explore the medical applications of the WAP peptide, a wap gene transgenic Drosophila melanogaster was constructed. In wap-expressing flies, high expression levels of wap gene (> 100 times) were achieved, in contrast to those of control flies, by qRT-PCR analysis. The wap gene expression was associated with increased resistance to microbial infection and decreased bacterial numbers in the flies. In addition, the WAP protein extract from wap-expressing flies, compared with control protein extract from control flies, showed improved antimicrobial activities against broad Gram-positive and Gram-negative bacteria, including the clinical drug resistant bacterium of methicillin-resistant S. aureus (MRSA), improved protease inhibitor activities against crude proteinases and commercial proteinases, including elastase, subtilis proteinase A, and proteinase K in vitro, and improved growth rate and microbial resistance, as well as wound-healing in loach and mouse models. These results suggest that wap-expressing flies could be used as a food additive in aquaculture to prevent infections and a potential antibacterial for fighting drug-resistant bacteria.

  • 115. Li, Shu
    et al.
    Yang, Hongxi
    Guo, Yanan
    Wei, Fengjiang
    Yang, Xilin
    Li, Daiqing
    Li, Mingzhen
    Xu, Weili
    Stockholm University, Faculty of Social Sciences, Aging Research Center (ARC), (together with KI).
    Li, Weidong
    Sun, Li
    Gao, Ying
    Wang, Yaogang
    Comparative efficacy and safety of urate-lowering therapy for the treatment of hyperuricemia: a systematic review and network meta-analysis2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 33082Article, review/survey (Refereed)
    Abstract [en]

    The prevalence of hyperuricemia and gout has been increasing, but the comparative effectiveness and safety of different treatments remain uncertain. We aimed to compare the effectiveness and safety of different treatments for hyperuricemia using network meta-analysis methodology. We systematically reviewed fifteen randomized controlled trials (involving 7,246 patients through January 2016) that compared the effects of different urate-lowering drugs (allopurinol, benzbromarone, febuxostat, pegloticase and probenecid) on hyperuricemia. Drug efficacy and safety, as outcomes, were measured by whether the target level of serum urate acid was achieved and whether any adverse events occurred, respectively. We derived pooled effect sizes expressed as odds ratios (ORs) and 95% confidence intervals (CIs). The efficacy and safety of the drugs were ranked by cumulative ranking probabilities. Our findings show that febuxostat, benzbromarone, probenecid, pegloticase, and allopurinol were all highly effective at reducing the risk of hyperuricemia compared to placebo. Febuxostat had the best efficacy and safety compared to the other drugs. Furthermore, febuxostat 120 mg QD was more effective at achieving urate-lowering targets (OR: 0.17, 95% CI: 0.12-0.24) and safer (OR: 0.72, 95% CI: 0.56-0.91) than allopurinol.

  • 116.
    Lind, Johan
    et al.
    Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution. Stockholm University, Faculty of Science, Department of Zoology.
    Lindenfors, Patrik
    Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution. Stockholm University, Faculty of Science, Department of Zoology.
    Ghirlanda, Stefano
    Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution. Brooklyn College, USA.
    Lidén, Kerstin
    Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution. Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Enquist, Magnus
    Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution. Stockholm University, Faculty of Science, Department of Zoology.
    Dating human cultural capacity using phylogenetic principles2013In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 3, article id 1785Article in journal (Refereed)
    Abstract [en]

    Humans have genetically based unique abilities making complex culture possible; an assemblage of traits which we term cultural capacity. The age of this capacity has for long been subject to controversy. We apply phylogenetic principles to date this capacity, integrating evidence from archaeology, genetics, paleoanthropology, and linguistics. We show that cultural capacity is older than the first split in the modern human lineage, and at least 170,000 years old, based on data on hyoid bone morphology, FOXP2 alleles, agreement between genetic and language trees, fire use, burials, and the early appearance of tools comparable to those of modern hunter-gatherers. We cannot exclude that Neanderthals had cultural capacity some 500,000 years ago. A capacity for complex culture, therefore, must have existed before complex culture itself. It may even originated long before. This seeming paradox is resolved by theoretical models suggesting that cultural evolution is exceedingly slow in its initial stages.

  • 117.
    Lindner, Philip
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Psychology, Clinical psychology. Karolinska Institutet, Sweden; Stockholm Center for Dependence Disorders, Stockholm County Council, Sweden.
    Flodin, Pär
    Larm, Peter
    Budhiraja, Meenal
    Savic-Berglund, Ivanka
    Jokinen, Jussi
    Tiihonen, Jari
    Hodgins, Sheilagh
    Amygdala-orbitofrontal structural and functional connectivity in females with anxiety disorders, with and without a history of conduct disorder2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 1101Article in journal (Refereed)
    Abstract [en]

    Conduct disorder (CD) and anxiety disorders (ADs) are often comorbid and both are characterized by hyper-sensitivity to threat, and reduced structural and functional connectivity between the amygdala and orbitofrontal cortex (OFC). Previous studies of CD have not taken account of ADs nor directly compared connectivity in the two disorders. We examined three groups of young women: 23 presenting CD and lifetime AD; 30 presenting lifetime AD and not CD; and 17 with neither disorder (ND). Participants completed clinical assessments and diffusion-weighted and resting-state functional MRI scans. The uncinate fasciculus was reconstructed using tractography and manual dissection, and structural measures extracted. Correlations of resting-state activity between amygdala and OFC seeds were computed. The CD + AD and AD groups showed similarly reduced structural integrity of the left uncinate compared to ND, even after adjusting for IQ, psychiatric comorbidity, and childhood maltreatment. Uncinate integrity was associated with harm avoidance traits among AD-only women, and with the interaction of poor anger control and anxiety symptoms among CD + AD women. Groups did not differ in functional connectivity. Reduced uncinate integrity observed in CD + AD and AD-only women may reflect deficient emotion regulation in response to threat, common to both disorders, while other neural mechanisms determine the behavioral response.

  • 118.
    Lindström, Ida
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Andersson, Eva
    Dogan, Jakob
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    The transition state structure for binding between TAZ1 of CBP and the disordered Hif-1 alpha CAD2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 7872Article in journal (Refereed)
    Abstract [en]

    Intrinsically disordered proteins (IDPs) are common in eukaryotes. However, relatively few experimental studies have addressed the nature of the rate-limiting transition state for the coupled binding and folding reactions involving IDPs. By using site-directed mutagenesis in combination with kinetics measurements we have here characterized the transition state for binding between the globular TAZ1 domain of CREB binding protein and the intrinsically disordered C-terminal activation domain of Hif-1 alpha (Hif-1 alpha CAD). A total of 17 Hif-1 alpha CAD point-mutations were generated and a F-value binding analysis was carried out. We found that native hydrophobic binding interactions are not formed at the transition state. We also investigated the effect the biologically important Hif-1 alpha CAD Asn-803 hydroxylation has on the binding kinetics, and found that the whole destabilization effect due the hydroxylation is within the dissociation rate constant. Thus, the rate-limiting transition state is disordered-like, with native hydrophobic binding contacts being formed cooperatively after the rate-limiting barrier, which is clearly shown by linear free energy relationships. The same behavior was observed in a previously characterized TAZ1/IDP interaction, which may suggest common features for the rate-limiting transition state for TAZ1/IDP interactions.

  • 119.
    Liu, Yiting
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Liao, Sifang
    Stockholm University, Faculty of Science, Department of Zoology.
    Veenstra, Jan A.
    Nässel, Dick R.
    Stockholm University, Faculty of Science, Department of Zoology.
    Drosophila insulin-like peptide 1 (DILP1) is transiently expressed during non-feeding stages and reproductive dormancy2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 26620Article in journal (Refereed)
    Abstract [en]

    The insulin/insulin-like growth factor signaling pathway is evolutionarily conserved in animals, and is part of nutrient-sensing mechanisms that control growth, metabolism, reproduction, stress responses, and lifespan. In Drosophila, eight insulin-like peptides (DILP1-8) are known, six of which have been investigated in some detail, whereas expression and functions of DILP1 and DILP4 remain enigmatic. Here we demonstrate that dilp1/DILP1 is transiently expressed in brain insulin producing cells (IPCs) from early pupa until a few days of adult life. However, in adult female flies where diapause is triggered by low temperature and short days, within a time window 0-10h post-eclosion, the dilp1/DILP1 expression remains high for at least 9 weeks. The dilp1 mRNA level is increased in dilp2, 3, 5 and dilp6 mutant flies, indicating feedback regulation. Furthermore, the DILP1 expression in IPCs is regulated by short neuropeptide F, juvenile hormone and presence of larval adipocytes. Male dilp1 mutant flies display increased lifespan and reduced starvation resistance, whereas in female dilp1 mutants oviposition is reduced. Thus, DILP1 is expressed in non-feeding stages and in diapausing flies, is under feedback regulation and appears to play sex-specific functional roles.

  • 120. Llopis-Torregrosa, Vicent
    et al.
    Vaz, Catarina
    Monteoliva, Lucia
    Ryman, Kicki
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Engström, Ylva
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Gacser, Attila
    Gil, Concha
    Ljungdahl, Per O.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Sychrova, Hana
    Trk1-mediated potassium uptake contributes to cell-surface properties and virulence of Candida glabrata2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 7529Article in journal (Refereed)
    Abstract [en]

    The absence of high-affinity potassium uptake in Candida glabrata, the consequence of the deletion of the TRK1 gene encoding the sole potassium-specific transporter, has a pleiotropic effect. Here, we show that in addition to changes in basic physiological parameters (e.g., membrane potential and intracellular pH) and decreased tolerance to various cell stresses, the loss of high affinity potassium uptake also alters cell-surface properties, such as an increased hydrophobicity and adherence capacity. The loss of an efficient potassium uptake system results in diminished virulence as assessed by two insect host models, Drosophila melanogaster and Galleria mellonella, and experiments with macrophages. Macrophages kill trk1 Delta cells more effectively than wild type cells. Consistently, macrophages accrue less damage when co-cultured with trk1 Delta mutant cells compared to wild-type cells. We further show that low levels of potassium in the environment increase the adherence of C. glabrata cells to polystyrene and the propensity of C. glabrata cells to form biofilms.

  • 121.
    Lu, Xin
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Sociology. National University of Defense Technology, China; Flowminder Foundation, Sweden; Karolinska Institutet, Sweden.
    Brelsford, Christa
    Network Structure and Community Evolution on Twitter: Human Behavior Change in Response to the 2011 Japanese Earthquake and Tsunami2014In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 4, p. 6773-Article in journal (Refereed)
    Abstract [en]

    To investigate the dynamics of social networks and the formation and evolution of online communities in response to extreme events, we collected three datasets from Twitter shortly before and after the 2011 earthquake and tsunami in Japan. We find that while almost all users increased their online activity after the earthquake, Japanese speakers, who are assumed to be more directly affected by the event, expanded the network of people they interact with to a much higher degree than English speakers or the global average. By investigating the evolution of communities, we find that the behavior of joining or quitting a community is far from random: users tend to stay in their current status and are less likely to join new communities from solitary or shift to other communities from their current community. While non-Japanese speakers did not change their conversation topics significantly after the earthquake, nearly all Japanese users changed their conversations to earthquake-related content. This study builds a systematic framework for investigating human behaviors under extreme events with online social network data and our findings on the dynamics of networks and communities may provide useful insight for understanding how patterns of social interaction are influenced by extreme events.

  • 122.
    Lu, Xin
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Sociology. National University of Defense Technology, China; Flowminder Foundation, Sweden; Karolinska Institutet, Sweden.
    Wetter, Erik
    Bharti, Nita
    Tatem, Andrew J.
    Bengtsson, Linus
    Approaching the Limit of Predictability in Human Mobility2013In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 3, article id 2923Article in journal (Refereed)
    Abstract [en]

    In this study we analyze the travel patterns of 500,000 individuals in Cote d'Ivoire using mobile phone call data records. By measuring the uncertainties of movements using entropy, considering both the frequencies and temporal correlations of individual trajectories, we find that the theoretical maximum predictability is as high as 88%. To verify whether such a theoretical limit can be approached, we implement a series of Markov chain (MC) based models to predict the actual locations visited by each user. Results show that MC models can produce a prediction accuracy of 87% for stationary trajectories and 95% for non-stationary trajectories. Our findings indicate that human mobility is highly dependent on historical behaviors, and that the maximum predictability is not only a fundamental theoretical limit for potential predictive power, but also an approachable target for actual prediction accuracy.

  • 123.
    Lundin, Erik J.
    et al.
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry. Umeå University, Sweden.
    Klaminder, J.
    Bastviken, D.
    Olid, C.
    Hansson, S. V.
    Karlsson, J.
    Large difference in carbon emission - burial balances between boreal and arctic lakes2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 14248Article in journal (Refereed)
    Abstract [en]

    Lakes play an important role in the global carbon (C) cycle by burying C in sediments and emitting CO2 and CH4 to the atmosphere. The strengths and control of these fundamentally different pathways are therefore of interest when assessing the continental C balance and its response to environmental change. In this study, based on new high-resolution estimates in combination with literature data, we show that annual emission: burial ratios are generally ten times higher in boreal compared to subarctic - arctic lakes. These results suggest major differences in lake C cycling between biomes, as lakes in warmer boreal regions emit more and store relatively less C than lakes in colder arctic regions. Such effects are of major importance for understanding climatic feedbacks on the continental C sink - source function at high latitudes. If predictions of global warming and northward expansion of the boreal biome are correct, it is likely that increasing C emissions from high latitude lakes will partly counteract the presumed increasing terrestrial C sink capacity at high latitudes.

  • 124. Lundin, Sverker
    et al.
    Gruselius, Joel
    Nystedt, Björn
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Lexow, Preben
    Käller, Max
    Lundeberg, Joakim
    Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing2013In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 3, article id 1186Article in journal (Refereed)
    Abstract [en]

    Here we demonstrate the use of short-read massive sequencing systems to in effect achieve longer read lengths through hierarchical molecular tagging. We show how indexed and PCR-amplified targeted libraries are degraded, sub-sampled and arrested at timed intervals to achieve pools of differing average length, each of which is indexed with a new tag. By this process, indices of sample origin, molecular origin, and degree of degradation is incorporated in order to achieve a nested hierarchical structure, later to be utilized in the data processing to order the reads over a longer distance than the sequencing system originally allows. With this protocol we show how continuous regions beyond 3000 bp can be decoded by an Illumina sequencing system, and we illustrate the potential applications by calling variants of the lambda genome, analysing TP53 in cancer cell lines, and targeting a variable canine mitochondrial region.

  • 125. Luo, Yi
    et al.
    Zhong, Mao Jun
    Huang, Yan
    Li, Feng
    Liao, Wen Bo
    Kotrschal, Alexander
    Stockholm University, Faculty of Science, Department of Zoology.
    Seasonality and brain size are negatively associated in frogs: evidence for the expensive brain framework2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 16629Article in journal (Refereed)
    Abstract [en]

    The challenges of seasonal environments are thought to contribute to brain evolution, but in which way is debated. According to the Cognitive Buffer Hypothesis (CBH) brain size should increase with seasonality, as the cognitive benefits of a larger brain should help overcoming periods of food scarcity via, for instance, increased behavioral flexibility. However, in line with the Expensive Brain Framework (EBF) brain size should decrease with seasonality because a smaller brain confers energetic benefits in periods of food scarcity. Empirical evidence is inconclusive and mostly limited to homoeothermic animals. Here we used phylogenetic comparative analyses to test the impact of seasonality on brain evolution across 30 species of anurans (frogs) experiencing a wide range of temperature and precipitation. Our results support the EBF because relative brain size and the size of the optic tectum were negatively correlated with variability in temperature. In contrast, we found no association between the variability in precipitation and the length of the dry season with either brain size or the sizes of other major brain regions. We suggest that seasonality-induced food scarcity resulting from higher variability in temperature constrains brain size evolution in anurans. Less seasonal environments may therefore facilitate the evolution of larger brains in poikilothermic animals.

  • 126. López-Bao, José Vicente
    et al.
    Aronsson, Malin
    Stockholm University, Faculty of Science, Department of Zoology. Swedish University of Agricultural Sciences, Sweden.
    Linnell, John D. C.
    Odden, John
    Persson, Jens
    Andrén, Henrik
    Eurasian lynx fitness shows little variation across Scandinavian human-dominated landscapes2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 8903Article in journal (Refereed)
    Abstract [en]

    Despite extensive research on the ecology and behavioural adaptations of large carnivores in human-dominated landscapes, information about the fitness consequences of sharing landscapes is still limited. We assessed the variation in three consecutive components of female fitness: the probability of reproduction, litter size and juvenile survival in relation to environmental and human factors in a solitary carnivore, the Eurasian lynx (Lynx lynx), occurring in human-dominated landscapes in Scandinavia. We used demographic data from 57 radio-collared adult females between 1995-2011 (126 radio-years). Overall, the yearly probability of female reproduction was 0.80, mean litter size was 2.34 (range 1-4) and the probability to find a female that reproduced in the spring being accompanied by at least one offspring during the subsequent winter was 0.70. We did not find evidence that food availability was a key factor influencing female fitness. Female lynx may adapt to food availability when establishing their home ranges by adopting an obstinate strategy, ensuring a minimum amount of prey necessary for survival and reproduction even during periods of prey scarcity. In human-dominated landscapes, where sufficient prey are available for lynx, mortality risk may have a larger influence on lynx population dynamics compared to food availability. Our results suggest that lynx population dynamics in human-dominated landscapes may be mainly driven by human impacts on survival.

  • 127. Ma, Fei
    et al.
    Wu, Tianfeng
    Zhao, Jiangang
    Song, Aili
    Liu, Huan
    Xu, Weili
    Stockholm University, Faculty of Social Sciences, Aging Research Center (ARC), (together with KI). Tianjin Medical University, China.
    Huang, Guowei
    Folic acid supplementation improves cognitive function by reducing the levels of peripheral inflammatory cytokines in elderly Chinese subjects with MCI2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 37486Article in journal (Refereed)
    Abstract [en]

    This study aimed to evaluate whether folic acid supplementation would improve cognitive performance by reducing serum inflammatory cytokine concentrations. This RCT was performed in Tianjin, China. Participants with mild cognitive impairment (MCI) were randomly assigned to the folic acid (400 mu g/day) or conventional treatment groups. Neuropsychological tests were administered, and folate, homocysteine, vitamin B-12, IL-6, TNF-alpha, A beta-42, and A beta-40 were measured at baseline and at 6- and 12-month time points. 152 participants (folic acid: 77, conventional: 75) completed the trial. Significant improvements in folate (eta p(2) = 0.703, P = 0.011), homocysteine (eta p(2) = 0.644, P = 0.009), A beta-42 (eta p(2) = 0.687, P = 0.013), peripheral IL-6 (eta p(2) = 0.477, P = 0.025), TNF-alpha (eta p(2) = 0.709, P = 0.009) levels were observed in folic acid group compared with conventional group. Folic acid supplementation improved the Full Scale Intelligence Quotient (P = 0.028; effect size d = 0.153), Information (P = 0.031; d = 0.157) and Digit Span (P = 0.009; d = 0.172) scores at 12 months compared with conventional treatment. Based on these findings, daily oral administration of a 400-mu g folic acid supplement to MCI subjects for 12 months can significantly improve cognitive performance and reduce peripheral inflammatory cytokine levels.

  • 128.
    Magnusson Hanson, Linda L.
    et al.
    Stockholm University, Faculty of Social Sciences, Stress Research Institute.
    Westerlund, Hugo
    Stockholm University, Faculty of Social Sciences, Stress Research Institute. Karolinska Institutet, Sweden.
    Goldberg, Marcel
    Zins, Marie
    Vahtera, Jussi
    Hulvej Rod, Naja
    Stenholm, Sari
    Steptoe, Andrew
    Kivimäki, Mika
    Work stress, anthropometry, lung function, blood pressure, and blood-based biomarkers: a cross-sectional study of 43,593 French men and women2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 9282Article in journal (Refereed)
    Abstract [en]

    Work stress is a risk factor for cardio-metabolic diseases, but few large-scale studies have examined the clinical profile of individuals with work stress. To address this limitation, we conducted a cross-sectional study including 43,593 working adults from a French population-based sample aged 18-72 years (the CONSTANCES cohort). According to the Effort-Reward Imbalance model, work stress was defined as an imbalance between perceived high efforts and low rewards at work. A standardized health examination included measures of anthropometry, lung function, blood pressure and standard blood-based biomarkers. Linear regression analyses before and after multivariable adjustment for age, socioeconomic status, depressive symptoms, health-related behaviours, and chronic conditions showed that work stress was associated with higher BMI, waist circumference, waist-hip ratio, alanine transaminase, white blood cell count and lower high-density lipoprotein cholesterol in men, and with higher BMI and white blood cell count in women (differences 0.03-0.06 standard deviations, P < 0.05 between individuals with and without work stress). No robust associations were observed with lung function, haemoglobin, creatinine, glucose levels or resting blood pressure measures. This indicates that work stress is associated altered metabolic profile, increased systemic inflammation, and, in men, poorer liver function, which is a marker of high alcohol consumption.

  • 129. Maleki, Shohreh
    et al.
    Kjellqvist, Sanela
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Paloschi, Valentina
    Magné, Joelle
    Branca, Rui Miguel Mamede
    Du, Lei
    Hultenby, Kjell
    Petrini, Johan
    Fuxe, Jonas
    Lehtiö, Janne
    Franco-Cereceda, Anders
    Eriksson, Per
    Björck, Hanna M.
    Mesenchymal state of intimal cells may explain higher propensity to ascending aortic aneurysm in bicuspid aortic valves2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 35712Article in journal (Refereed)
    Abstract [en]

    Individuals with a bicuspid aortic valve (BAV) are at significantly higher risk of developing aortic complications than individuals with tricuspid aortic valves (TAV) and defective signaling during the embryonic development and/or life time exposure to abnormal hemodynamic have been proposed as underlying factors. However, an explanation for the molecular mechanisms of aortopathy in BAV has not yet been provided. We combined proteomics, RNA analyses, immunohistochemistry, and electron microscopy to identify molecular differences in samples of non-dilated ascending aortas from BAV (N = 62) and TAV (N = 54) patients. Proteomic analysis was also performed for dilated aortas (N = 6 BAV and N = 5 TAV) to gain further insight into the aortopathy of BAV. Our results collectively showed the molecular signature of an endothelial/epithelial-mesenchymal (EndMT/EMT) transition-like process, associated with instability of intimal cell junctions and activation of RHOA pathway in the intima and media layers of ascending aorta in BAV patients. We propose that an improper regulation of EndMT/EMT during the spatiotemporally related embryogenesis of semilunar valves and ascending aorta in BAV individuals may result in aortic immaturity and instability prior to dilation. Exasperation of EndMT/EMT state in post embryonic life and/or exposure to non-physiological hemodynamic could lead to the aneurysm of ascending aorta in BAV individuals.

  • 130. Margus, Aigi
    et al.
    Piiroinen, Saija
    Lehmann, Philipp
    Stockholm University, Faculty of Science, Department of Zoology. University of Jyväskylä, Finland.
    Tikka, Santtu
    Karvanen, Juha
    Lindström, Leena
    Sublethal Pyrethroid Insecticide Exposure Carries Positive Fitness Effects Over Generations in a Pest Insect2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 11320Article in journal (Refereed)
    Abstract [en]

    Stress tolerance and adaptation to stress are known to facilitate species invasions. Many invasive species are also pests and insecticides are used to control them, which could shape their overall tolerance to stress. It is well-known that heavy insecticide usage leads to selection of resistant genotypes but less is known about potential effects of mild sublethal insecticide usage. We studied whether stressful, sublethal pyrethroid insecticide exposure has within-generational and/or maternal transgenerational effects on fitness-related traits in the Colorado potato beetle (Leptinotarsa decemlineata) and whether maternal insecticide exposure affects insecticide tolerance of offspring. Sublethal insecticide stress exposure had positive within-and transgenerational effects. Insecticide-stressed larvae had higher adult survival and higher adult body mass than those not exposed to stress. Furthermore, offspring whose mothers were exposed to insecticide stress had higher larval and pupal survival and were heavier as adults (only females) than those descending from control mothers. Maternal insecticide stress did not explain differences in lipid content of the offspring. To conclude, stressful insecticide exposure has positive transgenerational fitness effects in the offspring. Therefore, unsuccessful insecticide control of invasive pest species may lead to undesired side effects since survival and higher body mass are known to facilitate population growth and invasion success.

  • 131.
    Marques, B.
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Universidade Federal de Minas Gerais, Brazil.
    Matoso, A. A.
    Pimenta, W. M.
    Gutierrez-Esparza, A. J.
    Santos, M. F.
    Padua, S.
    Experimental simulation of decoherence in photonics qudits2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 16049Article in journal (Refereed)
    Abstract [en]

    We experimentally perform the simulation of open quantum dynamics in single-qudit systems. Using a spatial light modulator as a dissipative optical device, we implement dissipative-dynamical maps onto qudits encoded in the transverse momentum of spontaneous parametric down-converted photon pairs. We show a well-controlled technique to prepare entangled qudits states as well as to implement dissipative local measurements; the latter realize two specific dynamics: dephasing and amplitude damping. Our work represents a new analogy-dynamical experiment for simulating an open quantum system.

  • 132.
    Masuyer, Geoffrey
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Zhang, Sicai
    Barkho, Sulyman
    Shen, Yi
    Henriksson, Linda
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Košenina, Sara
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Dong, Min
    Stenmark, Pål
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Structural characterisation of the catalytic domain of botulinum neurotoxin X - high activity and unique substrate specificity2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 4518Article in journal (Refereed)
    Abstract [en]

    Botulinum neurotoxins (BoNTs) are among the most potent toxins known and are also used to treat an increasing number of medical disorders. There are seven well-established serotypes (BoNT/A-G), which all act as zinc-dependent endopeptidases targeting specific members of the SNARE proteins required for synaptic vesicle exocytosis in neurons. A new toxin serotype, BoNT/X, was recently identified. It cleaves not only the canonical targets, vesicle associated membrane proteins (VAMP) 1/2/3 at a unique site, but also has the unique ability to cleave VAMP4/5 and Ykt6. Here we report the 1.35 angstrom X-ray crystal structure of the light chain of BoNT/X (LC/X). LC/X shares the core fold common to all other BoNTs, demonstrating that LC/X is a bona fide member of BoNT-LCs. We found that access to the catalytic pocket of LC/X is more restricted, and the regions lining the catalytic pocket are not conserved compared to other BoNTs. Kinetic studies revealed that LC/X cleaves VAMP1 with a ten times higher efficiency than BoNT/B and the tetanus neurotoxin. The structural information provides a molecular basis to understand the convergence/divergence between BoNT/X and other BoNTs, to develop effective LC inhibitors, and to engineer new scientific tools and therapeutic toxins targeting distinct SNARE proteins in cells.

  • 133.
    Mata Forsberg, Manuel
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Björkander, Sophia
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Pang, Yanhong
    Lundqvist, Ludwig
    Ndi, Mama
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Ott, Martin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Escribá, Irene Buesa
    Jaeger, Marie-Charlotte
    Roos, Stefan
    Sverremark-Ekström, Eva
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Extracellular membrane vesicles from lactobacilli dampen IFN-γ responses in a monocyte-dependent mannerIn: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322Article in journal (Refereed)
  • 134. Matricon, Pierre
    et al.
    Ranganathan, Anirudh
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Warnick, Eugene
    Gao, Zhan-Guo
    Rudling, Axel
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Lambertucci, Catia
    Marucci, Gabriella
    Ezzati, Aitakin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Jaiteh, Mariama
    Dal Ben, Diego
    Jacobson, Kenneth A.
    Carlsson, Jens
    Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A(2A) adenosine receptor binding site2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 6398Article in journal (Refereed)
    Abstract [en]

    Fragment-based lead discovery is becoming an increasingly popular strategy for drug discovery. Fragment screening identifies weakly binding compounds that require optimization to become high-affinity leads. As design of leads from fragments is challenging, reliable computational methods to guide optimization would be invaluable. We evaluated using molecular dynamics simulations and the free energy perturbation method (MD/FEP) in fragment optimization for the A(2A) adenosine receptor, a pharmaceutically relevant G protein-coupled receptor. Optimization of fragments exploring two binding site subpockets was probed by calculating relative binding affinities for 23 adenine derivatives, resulting in strong agreement with experimental data (R-2 = 0.78). The predictive power of MD/FEP was significantly better than that of an empirical scoring function. We also demonstrated the potential of the MD/FEP to assess multiple binding modes and to tailor the thermodynamic profile of ligands during optimization. Finally, MD/FEP was applied prospectively to optimize three nonpurine fragments, and predictions for 12 compounds were evaluated experimentally. The direction of the change in binding affinity was correctly predicted in a majority of the cases, and agreement with experiment could be improved with rigorous parameter derivation. The results suggest that MD/FEP will become a powerful tool in structure-driven optimization of fragments to lead candidates.

  • 135.
    Maïno, Nicolas
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). Lunaphore Technologies SA, Switzerland.
    Hauling, Thomas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). University College London, United Kingdom.
    Cappi, G.
    Madaboosi, Narayanan
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Dupouy, D. G.
    Nilsson, Mats
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    A microfluidic platform towards automated multiplexed in situ sequencing2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 3542Article in journal (Refereed)
    Abstract [en]

    Advancements in multiplexed in situ RNA profiling techniques have given unprecedented insight into spatial organization of tissues by enabling single-molecule quantification and sub-micron localization of dozens to thousands of RNA species simultaneously in cells and entire tissue sections. However, the lack of automation of the associated complex experimental procedures represents a potential hurdle towards their routine use in laboratories. Here, we demonstrate an approach towards automated generation and sequencing of barcoded mRNA amplicons in situ, directly in fixed cells. This is achieved through adaptation of a microfluidic tool compatible with standard microscope slides and cover glasses. The adapted tool combines a programmable reagent delivery system with temperature controller and flow cell to perform established in situ sequencing protocols, comprising hybridization and ligation of gene-specific padlock probes, rolling circle amplification of the probes yielding barcoded amplicons and identification of amplicons through barcode sequencing. By adapting assay parameters (e.g. enzyme concentration and temperature), we achieve a near-identical performance in identifying mouse beta-actin transcripts, in comparison with the conventional manual protocol. The technically adapted assay features i) higher detection efficiency, ii) shorter protocol time, iii) lower consumption of oligonucleotide reagents but slightly more enzyme. Such an automated microfluidic tissue processor for in situ sequencing studies would greatly enhance its research potentials especially for cancer diagnostics, thus paving way to rapid and effective therapies.

  • 136. McLean, Kyle Jarrod
    et al.
    Straimer, Judith
    Hopp, Christine S.
    Vega-Rodriguez, Joel
    Small-Saunders, Jennifer L.
    Kanatani, Sachie
    Tripathi, Abhai
    Mlambo, Godfree
    Dumoulin, Peter C.
    Harris, Chantal T.
    Tong, Xinran
    Shears, Melanie J.
    Ankarklev, Johan
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Weill Cornell School of Medicine, USA.
    Kafsack, Bjorn F. C.
    Fidock, David A.
    Sinnis, Photini
    Generation of Transmission-Competent Human Malaria Parasites with Chromosomally-Integrated Fluorescent Reporters2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 13131Article in journal (Refereed)
    Abstract [en]

    Malaria parasites have a complex life cycle that includes specialized stages for transmission between their mosquito and human hosts. These stages are an understudied part of the lifecycle yet targeting them is an essential component of the effort to shrink the malaria map. The human parasite Plasmodium falciparum is responsible for the majority of deaths due to malaria. Our goal was to generate transgenic P. falciparum lines that could complete the lifecycle and produce fluorescent transmission stages for more in-depth and high-throughput studies. Using zinc-finger nuclease technology to engineer an integration site, we generated three transgenic P. falciparum lines in which tdtomato or gfp were stably integrated into the genome. Expression was driven by either stage-specific peg4 and csp promoters or the constitutive ef1 alpha promoter. Phenotypic characterization of these lines demonstrates that they complete the life cycle with high infection rates and give rise to fluorescent mosquito stages. The transmission stages are sufficiently bright for intra-vital imaging, flow cytometry and scalable screening of chemical inhibitors and inhibitory antibodies.

  • 137. Mincigrucci, Riccardo
    et al.
    Kowalewski, Markus
    University of California, USA.
    Rouxel, Jérémy R.
    Bencivenga, Filippo
    Mukamel, Shaul
    Masciovecchio, Claudio
    Impulsive UV-pump/X-ray probe study of vibrational dynamics in glycine2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 15466Article in journal (Refereed)
    Abstract [en]

    We report an ab-initio study of a pump-probe experiment on the amino-acid glycine. We consider an UV pump followed by an X-ray probe tuned to carbon K-edge and study the vibronic structure of the core transition. The simulated experiment is feasible using existing free electron laser or high harmonic generation sources and thanks to the localization of the core orbitals posseses chemical selectivity. The present theory applies to other experimental schemes, including the use of a THz probe, available with present soft X-ray free electron lasers and/or high harmonic generation sources.

  • 138. Moon, Woosok
    et al.
    Wettlaufer, John S.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Yale University, USA; University of Oxford, UK.
    A unified nonlinear stochastic time series analysis for climate science2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 44228Article in journal (Refereed)
    Abstract [en]

    Earth's orbit and axial tilt imprint a strong seasonal cycle on climatological data. Climate variability is typically viewed in terms of fluctuations in the seasonal cycle induced by higher frequency processes. We can interpret this as a competition between the orbitally enforced monthly stability and the fluctuations/noise induced by weather. Here we introduce a new time-series method that determines these contributions from monthly-averaged data. We find that the spatio-temporal distribution of the monthly stability and the magnitude of the noise reveal key fingerprints of several important climate phenomena, including the evolution of the Arctic sea ice cover, the El Nino Southern Oscillation (ENSO), the Atlantic Nino and the Indian Dipole Mode. In analogy with the classical destabilising influence of the ice-albedo feedback on summertime sea ice, we find that during some time interval of the season a destabilising process operates in all of these climate phenomena. The interaction between the destabilisation and the accumulation of noise, which we term the memory effect, underlies phase locking to the seasonal cycle and the statistical nature of seasonal predictability.

  • 139.
    Moreno, Claudia R. C.
    et al.
    Stockholm University, Faculty of Social Sciences, Stress Research Institute. University of São Paulo, Brazil.
    Vasconcelos, S.
    Marqueze, E. C.
    Lowden, Arne
    Stockholm University, Faculty of Social Sciences, Stress Research Institute.
    Middleton, B.
    Fischer, M.
    Louzada, F. M.
    Skene, D. J.
    Sleep patterns in Amazon rubber tappers with and without electric light at home2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 14074Article in journal (Refereed)
    Abstract [en]

    Today's modern society is exposed to artificial electric lighting in addition to the natural light-dark cycle. Studies assessing the impact of electric light exposure on sleep and its relation to work hours are rare due to the ubiquitous presence of electricity. Here we report a unique study conducted in two phases in a homogenous group of rubber tappers living and working in a remote area of the Amazon forest, comparing those living without electric light (n = 243 in first phase; n = 25 in second phase) to those with electric light at home (n = 97 in first phase; n = 17 in second phase). Questionnaire data (Phase 1) revealed that rubber tappers with availability of electric light had significantly shorter sleep on work days (30 min/day less) than those without electric light. Analysis of the data from the Phase 2 sample showed a significant delay in the timing of melatonin onset in workers with electric light compared to those without electric light (p < 0.01). Electric lighting delayed sleep onset and reduced sleep duration during the work week and appears to interfere with alignment of the circadian timing system to the natural light/dark cycle.

  • 140.
    Motwani, Hitesh V.
    et al.
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Frostne, Cecilia
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Törnqvist, Margareta
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Parallelogram based approach for in vivo dose estimation of genotoxic metabolites in humans with relevance to reduction of animal experiments2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 17560Article in journal (Refereed)
    Abstract [en]

    When employing metabolism studies of genotoxic compounds/metabolites and cancer tests for risk estimation, low exposure doses in humans are roughly extrapolated from high exposure doses in animals. An improvement is to measure the in vivo dose, i.e. area under concentration-time curve (AUC), of the causative genotoxic agent. In the present work, we propose and evaluate a parallelogram based approach for estimation of the AUC of genotoxic metabolites that incorporates in vitro metabolic data and existing knowledge from published in vivo data on hemoglobin (Hb) adduct levels, using glycidamide (GA) as a case study compound that is the genotoxic metabolite of acrylamide (AA). The estimated value of AUC of GA per AUC of AA from the parallelogram approach vs. that from Hb adduct levels measured in vivo were in good agreement; 0.087 vs. 0.23 in human and 1.4 vs. 0.53 in rat, respectively. The described parallelogram approach is simple, and can be useful to provide an approximate estimation of the AUC of metabolites in humans at low exposure levels for which sensitive methods for analyzing the metabolites are not available, as well as aid in reduction of animal experiments for metabolism studies that are to be used for cancer risk assessment.

  • 141.
    Motwani, Hitesh V.
    et al.
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Westberg, Emelie
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Törnqvist, Margareta
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Interaction of benzo[a] pyrene diol epoxide isomers with human serum albumin: Site specific characterisation of adducts and associated kinetics2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 36243Article in journal (Refereed)
    Abstract [en]

    Carcinogenicity of benzo[a] pyrene {B[a]P, a polycyclic aromatic hydrocarbon (PAH)} involves DNA-modification by B[a] P diol epoxide (BPDE) metabolites. Adducts to serum albumin (SA) are not repaired, unlike DNA adducts, and therefore considered advantageous in assessment of in vivo dose of BPDEs. In the present work, kinetic experiments were performed in relation to the dose (i.e. concentration over time) of different BPDE isomers, where human SA (hSA) was incubated with respective BPDEs under physiological conditions. A liquid chromatography (LC) tandem mass spectrometry methodology was employed for characterising respective BPDE-adducts at histidine and lysine. This strategy allowed to structurally distinguish between the adducts from racemic anti-and syn-BPDE and between (+)- and (-)-anti-BPDE, which has not been attained earlier. The adduct levels quantified by LC-UV and the estimated rate of disappearance of BPDEs in presence of hSA gave an insight into the reactivity of the diol epoxides towards the N-sites on SA. The structure specific method and dosimetry described in this work could be used for accurate estimation of in vivo dose of the BPDEs following exposure to B[a] P, primarily in dose response studies of genotoxicity, e.g. in mice, to aid in quantitative risk assessment of PAHs.

  • 142.
    Muheim, Claudio
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Götzke, Hansjörg
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Eriksson, Anna U.
    Lindberg, Stina
    Lauritsen, Ida
    Norholm, Morten H. H.
    Daley, Daniel O.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Increasing the permeability of Escherichia coli using MAC132432017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 17629Article in journal (Refereed)
    Abstract [en]

    The outer membrane of gram-negative bacteria is a permeability barrier that prevents the efficient uptake of molecules with large scaffolds. As a consequence, a number of antibiotic classes are ineffective against gram-negative strains. Herein we carried out a high throughput screen for small molecules that make the outer membrane of Escherichia coli more permeable. We identified MAC13243, an inhibitor of the periplasmic chaperone LolA that traffics lipoproteins from the inner to the outer membrane. We observed that cells were (1) more permeable to the fluorescent probe 1-N-phenylnapthylamine, and (2) more susceptible to large-scaffold antibiotics when sub-inhibitory concentrations of MAC13243 were used. To exclude the possibility that the permeability was caused by an off-target effect, we genetically reconstructed the MAC13243-phenotype by depleting LolA levels using the CRISPRi system.

  • 143. Mörner, Torsten
    et al.
    Hansson, Tomas
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Carlsson, Le
    Berg, Anna-Lena
    Ruiz Muñoz, Yolanda
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry. University of Vigo, Spain.
    Gustavsson, Hanna
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Mattsson, Roland
    Balk, Lennart
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Thiamine deficiency impairs common eider (Somateria mollissima) reproduction in the field2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 14451Article in journal (Refereed)
    Abstract [en]

    The Baltic Sea population of the common eider (Somateria mollissima) has declined dramatically during the last two decades. Recently, widespread episodic thiamine (vitamin B1) deficiency has been demonstrated in feral birds and suggested to contribute significantly to declining populations. Here we show that the decline of the common eider population in the Baltic Sea is paralleled by high mortality of the pulli a few days after hatch, owing to thiamine deficiency and probably also thereby associated abnormal behaviour resulting in high gull predation. An experiment with artificially incubated common eider eggs collected in the field revealed that thiamine treatment of pulli had a therapeutic effect on the thiamine status of the brain and prevented death. The mortality was 53% in untreated specimens, whereas it was only 7% in thiamine treated specimens. Inability to dive was also linked to brain damage typical for thiamine deficiency. Our results demonstrate how thiamine deficiency causes a range of symptoms in the common eider pulli, as well as massive die-offs a few days after hatch, which probably are the major explanation of the recent dramatic population declines.

  • 144. Nahar, Nurun
    et al.
    Westerberg, Erik
    Arif, Usman
    Huchelmann, Alexandre
    Guasca, Alexandra Olarte
    Beste, Lisa
    Dalman, Kerstin
    Dutta, Paresh C.
    Jonsson, Lisbeth
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Sitbon, Folke
    Transcript profiling of two potato cultivars during glycoalkaloid-inducing treatments shows differential expression of genes in sterol and glycoalkaloid metabolism2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 43268Article in journal (Refereed)
    Abstract [en]

    Steroidal glycoalkaloids (SGA) are sterol-derived neurotoxic defence substances present in several members of the Solanaceae. In the potato (Solanum tuberosum), high SGA levels may render tubers harmful for consumption. Tuber SGA levels depend on genetic factors, and can increase as a response to certain stresses and environmental conditions. To identify genes underlying the cultivar variation in tuber SGA levels, we investigated two potato cultivars differing in their SGA accumulation during wounding or light exposure; two known SGA-inducing treatments. Using microarray analysis coupled to sterol and SGA quantifications, we identified a small number of differentially expressed genes that were associated with increased SGA levels. Two of these genes, encoding distinct types of sterol Delta(24)-reductases, were by sense/antisense expression in transgenic potato plants shown to have differing roles in sterol and SGA metabolism. The results show that an increased SGA level in potato tubers during both wounding and light exposure is mediated by coordinated expression of a set of key genes in isoprenoid and steroid metabolism, and suggest that differences in this expression underlie cultivar variations in SGA levels. These results may find use within potato breeding and quality assessment.

  • 145.
    Nascimento, Francisco J. A.
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Bangor University, United Kingdom.
    Lallias, Delphine
    Bik, Holly M.
    Creer, Simon
    Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 11737Article in journal (Refereed)
    Abstract [en]

    Understanding how biodiversity changes in time and space is vital to assess the effects of environmental change on benthic ecosystems. Due to the limitations of morphological methods, there has been a rapid expansion in the application of high-throughput sequencing methods to study benthic eukaryotic communities. However, the effect of sample size and small-scale spatial variation on the assessment of benthic eukaryotic diversity is still not well understood. Here, we investigate the effect of different sample volumes in the genetic assessment of benthic metazoan and non-metazoan eukaryotic community composition. Accordingly, DNA was extracted from five different cumulative sediment volumes comprising 100% of the top 2 cm of five benthic sampling cores, and used as template for Ilumina MiSeq sequencing of 18 S rRNA amplicons. Sample volumes strongly impacted diversity metrics for both metazoans and non-metazoan eukaryotes. Beta-diversity of treatments using smaller sample volumes was significantly different from the beta-diversity of the 100% sampled area. Overall our findings indicate that sample volumes of 0.2 g (1% of the sampled area) are insufficient to account for spatial heterogeneity at small spatial scales, and that relatively large percentages of sediment core samples are needed for obtaining robust diversity measurement of both metazoan and non-metazoan eukaryotes.

  • 146.
    Nawareg, Mohamed
    et al.
    Stockholm University, Faculty of Science, Department of Physics. University of Gdansk, Poland.
    Muhammad, Sadiq
    Stockholm University, Faculty of Science, Department of Physics.
    Amselem, Elias
    Stockholm University, Faculty of Science, Department of Physics.
    Bourennane, Mohamed
    Stockholm University, Faculty of Science, Department of Physics.
    Experimental Measurement-Device-Independent Entanglement Detection2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 8048Article in journal (Refereed)
    Abstract [en]

    Entanglement is one of the most puzzling features of quantum theory and of great importance for the new field of quantum information. The determination whether a given state is entangled or not is one of the most challenging open problems of the field. Here we report on the experimental demonstration of measurement-device-independent (MDI) entanglement detection using witness method for general two qubits photon polarization systems. In the MDI settings, there is no requirement to assume perfect implementations or neither to trust the measurement devices. This experimental demonstration can be generalized for the investigation of properties of quantum systems and for the realization of cryptography and communication protocols.

  • 147.
    Neagu, Alexandra
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Tai, Cheuk-Wai
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Local disorder in Na0.5Bi0.5TiO3-piezoceramic determined by 3D electron diffuse scattering2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 12519Article in journal (Refereed)
    Abstract [en]

    Local structural distortions in Na0.5Bi0.5TiO3-based solid solutions have been proved to play a crucial role in understanding and tuning their enhanced piezoelectric properties near the morphotropic phase boundary. In this work all local structural disorders in a lead-free ternary system, namely 85% Na0.5Bi0.5TiO3-10% Bi0.5K0.5TiO3-5% BaTiO3, were mapped in reciprocal space by 3D electron diffraction. Furthermore, a comprehensive model of the local disorder was developed by analysing the intensity and morphology of the observed weak diffuse scattering. We found that the studied ceramics consists of plate-like in-phase oxygen octahedral nanoscale domains randomly distributed in an antiphase tilted matrix. In addition, A-site chemical short-range order of Na/Bi and polar displacements contribute to different kinds of diffuse scattering. The proposed model explains all the observed diffraction features and offers insight into the ongoing controversy over the nature of local structural distortions in Na0.5Bi0.5TiO3-based solid solutions.

  • 148. Nielsen, Steffen
    et al.
    Bassler, Niels
    Stockholm University, Faculty of Science, Department of Physics.
    Grzanka, Leszek
    Swakon, Jan
    Olko, Pawel
    Andreassen, Christian Nicolaj
    Alsner, Jan
    Sørensen, Brita Singers
    Optimal reference genes for normalization of qPCR gene expression data from proton and photon irradiated dermal fibroblasts2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 12688Article in journal (Refereed)
    Abstract [en]

    The transcriptional response of cells exposed to proton radiation is not equivalent to the response induced by traditional photon beams. Changes in cellular signalling is most commonly studied using the method Quantitative polymerase chain reaction (qPCR). Stable reference genes must be used to accurately quantify target transcript expression. The study aim was to identify suitable reference genes for normalisation of gene expression levels in normal dermal fibroblasts irradiated with either proton or photon beams. The online tool RefFinder was used to analyse and identify the most stably expressed genes from a panel of 22 gene candidates. To assess the reliability of the identified reference genes, a selection of the most and least stable reference genes was used to normalise target transcripts of interest. Fold change levels varied considerably depending on the used reference gene. The top ranked genes IPO8, PUM1, MRPL19 and PSMC4 produced highly similar target gene expression, while expression using the worst ranked genes, TFRC and HPRT1, was clearly modified due to reference gene instability.

  • 149.
    Nilsonne, Gustav
    et al.
    Stockholm University, Faculty of Social Sciences, Stress Research Institute. Karolinska Institutet, Sweden .
    Tamm, Sandra
    Stockholm University, Faculty of Social Sciences, Stress Research Institute. Karolinska Institutet, Sweden .
    Schwarz, Johanna
    Stockholm University, Faculty of Social Sciences, Stress Research Institute. Karolinska Institutet, Sweden .
    Almeida, Rita
    Fischer, Håkan
    Stockholm University, Faculty of Social Sciences, Department of Psychology, Biological psychology.
    Kecklund, Göran
    Stockholm University, Faculty of Social Sciences, Stress Research Institute.
    Lekander, Mats
    Stockholm University, Faculty of Social Sciences, Stress Research Institute. Karolinska Institutet, Sweden .
    Fransson, Peter
    Åkerstedt, Torbjörn
    Stockholm University, Faculty of Social Sciences, Stress Research Institute. Karolinska Institutet, Sweden .
    Intrinsic brain connectivity after partial sleep deprivation in young and older adults: results from the Stockholm Sleepy Brain study2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 9422Article in journal (Refereed)
    Abstract [en]

    Sleep deprivation has been reported to affect intrinsic brain connectivity, notably reducing connectivity in the default mode network. Studies to date have however shown inconsistent effects, in many cases lacked monitoring of wakefulness, and largely included young participants. We investigated effects of sleep deprivation on intrinsic brain connectivity in young and older participants. Participants aged 20–30 (final n = 30) and 65–75 (final n = 23) years underwent partial sleep deprivation (3 h sleep) in a cross-over design, with two 8-minutes eyes-open resting state functional magnetic resonance imaging (fMRI) runs in each session, monitored by eye-tracking. We assessed intrinsic brain connectivity using independent components analysis (ICA) as well as seed-region analyses of functional connectivity, and also analysed global signal variability, regional homogeneity, and the amplitude of low-frequency fluctuations. Sleep deprivation caused increased global signal variability. Changes in investigated resting state networks and in regional homogeneity were not statistically significant. Younger participants had higher connectivity in most examined networks, as well as higher regional homogeneity in areas including anterior and posterior cingulate cortex. In conclusion, we found that sleep deprivation caused increased global signal variability, and we speculate that this may be caused by wake-state instability.

  • 150.
    Nilsson, Tobias
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Rydström Lundin, Camilla
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Nordlund, Gustav
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Ädelroth, Pia
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    von Ballmoos, Christoph
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. University of Bern, Switzerland.
    Brzezinski, Peter
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Lipid-mediated Protein-protein Interactions Modulate Respiration-driven ATP Synthesis2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 24113Article in journal (Refereed)
    Abstract [en]

    Energy conversion in biological systems is underpinned by membrane-bound proton transporters that generate and maintain a proton electrochemical gradient across the membrane which used, e.g. for generation of ATP by the ATP synthase. Here, we have co-reconstituted the proton pump cytochrome bo3 (ubiquinol oxidase) together with ATP synthase in liposomes and studied the effect of changing the lipid composition on the ATP synthesis activity driven by proton pumping. We found that for 100 nm liposomes, containing 5 of each proteins, the ATP synthesis rates decreased significantly with increasing fractions of DOPA, DOPE, DOPG or cardiolipin added to liposomes made of DOPC; with e.g. 5% DOPG, we observed an almost 50% decrease in the ATP synthesis rate. However, upon increasing the average distance between the proton pumps and ATP synthases, the ATP synthesis rate dropped and the lipid dependence of this activity vanished. The data indicate that protons are transferred along the membrane, between cytochrome bo3 and the ATP synthase, but only at sufficiently high protein densities. We also argue that the local protein density may be modulated by lipid-dependent changes in interactions between the two proteins complexes, which points to a mechanism by which the cell may regulate the overall activity of the respiratory chain.

12345 101 - 150 of 210
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf